Trees
Gammmaproteobacteria Rectangular Tree
ggtree(tree_Gammaproteobacteria) +
geom_tiplab(size=3) +
xlim(0,20)

ggsave(
"Gammmaproteobacteria_Rectangular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria Circular Tree
ggtree(tree_Gammaproteobacteria, layout="circular") +
geom_tiplab(aes(angle=angle))+
theme_tree() +
xlim(0,20)

ggsave(
"Gammmaproteobacteria_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
NEON MAGS Gammaproteobacteria Highlight Circular Tree
ggtree(tree_bac, layout="circular") +
geom_hilight(node=3048, fill="steelblue", alpha=.6)

ggsave(
"NEON_MAGS_Gammaproteobacteria_Highlight_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
NEON MAGS Gammaproteobacteria Highlight with Label Circular
Tree
ggtree(tree_bac, layout="circular", branch.length="none") +
geom_hilight(node=3047, fill="grey", alpha=.6) +
geom_cladelab(node=3047, label="Pseudomonadota", align=TRUE, angle='auto',
offset.text=0.5 , textcolor='black', barcolor='grey',barsize=1.5, fontsize=5)+
geom_hilight(node=3048, fill="steelblue", alpha=.6) +
geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE, angle='auto', offset=1,
offset.text=0.5 , textcolor='black', barcolor='steelblue',barsize=1.5, fontsize=5)

ggsave(
"NEON_MAGS_Gammaproteobacteria_Highlight_with_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 14 in image
NEON MAGS Gammaproteobacteria Label Circular Tree
ggtree(tree_bac, layout="circular", branch.length="none") %>%
collapse(node=3048) +
geom_point2(aes(subset=(node==3048)), shape=23, size=5, fill='steelblue') +
geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE,
offset = 2, textcolor='steelblue')

ggsave(
"NEON_MAGS_Gammaproteobacteria_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
NEON MAGS Gammaproteobacteria Minimized Circular Tree
p <- ggtree(tree_bac, layout="circular", branch.length="none")
scaleClade(p, 3048, .2) %>% collapse(3048, 'min', fill="steelblue") +
geom_cladelab(node=3048, label="Gammaproteobacteria", align=TRUE,
offset = 0.2, textcolor='steelblue')

ggsave(
"NEON_MAGS_Gammaproteobacteria_Minimized_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Order Labels Circular Tree
ggtree(tree_Gammaproteobacteria, layout="circular") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tiplab(size=2, hjust=-.1) +
xlim(0,20) +
geom_point(mapping=aes(color=Order))

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Order_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Order and Assembly Type Labels Circular
Tree
ggtree(tree_Gammaproteobacteria, layout="circular") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tiplab(size=2, hjust=-.1) +
xlim(0,20) +
geom_point(mapping=aes(color=Order, shape = `Assembly Type`))
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point()`).

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Order_and_Assembly_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point()`).
Gammaproteobacteria with Ecosystem Subtype System Rectangular
Tree
ggtree(tree_Gammaproteobacteria) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tiplab(size=2, hjust=-.1) +
xlim(0,20) +
geom_point(mapping=aes(color=`Ecosystem Subtype`))

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_System_Rectangular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Site Location Rectangular Tree
ggtree(tree_Gammaproteobacteria) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tiplab(size=2, hjust=-.1) +
xlim(0,20) +
geom_point(mapping=aes(color=`Site.y`)) +labs(color="Site")

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Site_Location_Rectangular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Bin Completeness Label Rectangular
Tree
ggtree(tree_Gammaproteobacteria) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tippoint(aes(colour=`Bin Completeness`)) +
scale_colour_gradient(low='blue', high='red') +
geom_tiplab(size=2, hjust=-.1) +
xlim(0,20)

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Bin_Completeness_Label_Rectangular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Ecosystem Subtype and Total number of Bases
Label Circular Tree
ggtree(tree_Gammaproteobacteria, layout="circular") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`))
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_and_Total_Number_of_Bases_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).
Gammaproteobacteria triplot with Bin Completeness and Bin
Contamination
# For unknown reasons the following does not like blank spaces in the names
NEON_MAGs_metagenomes_chemistry_noblank <- NEON_MAGs_metagenomes_chemistry %>%
rename("AssemblyType" = "Assembly Type") %>%
rename("BinCompleteness" = "Bin Completeness") %>%
rename("BinContamination" = "Bin Contamination") %>%
rename("TotalNumberofBases" = "Total Number of Bases") %>%
rename("EcosystemSubtype" = "Ecosystem Subtype") %>%
rename("GeneCount" = "Gene Count") %>%
rename("GCassembled" = "GC * assembled")
ggtree(tree_Gammaproteobacteria) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tippoint(aes(colour=`Ecosystem Subtype`)) +
# For unknown reasons the following does not like blank spaces in the names
geom_facet(panel = "Bin Completeness", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point,
mapping=aes(x = BinCompleteness)) +
geom_facet(panel = "Bin Contamination", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col,
aes(x = BinContamination), orientation = 'y', width = .6) +
theme_tree2(legend.position=c(.1, .7))

ggsave(
"NEON_MAGS_Gammaproteobacteria_triplot_with_Bin_Completeness_and_Bin_Contamination.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria triplot with Gene and GC Content
ggtree(tree_Gammaproteobacteria) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tippoint(aes(colour=`Ecosystem Subtype`)) +
# For unknown reasons the following does not like blank spaces in the names
geom_facet(panel = "Gene Count", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point,
mapping=aes(x = GeneCount))+
geom_facet(panel = "% GC Content ", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col,
aes(x = GCassembled), orientation = 'y', width = .6) +
theme_tree2(legend.position=c(.1, .7))

ggsave(
"NEON_MAGS_Gammaproteobacteria_triplot_with_ Gene_and_GC_Content.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Gammaproteobacteria with Ecosystem Subtype and Total Number of Bases
in Outside Labels
ggtree(tree_Gammaproteobacteria, layout="circular", branch.length="none") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_tile,
mapping=aes(y=label, x=1, fill= AssemblyType),
offset=0.08, # The distance between external layers, default is 0.03 times of x range of tree.
pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
)
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"NEON_MAGS_Gammaproteobacteria_with_Ecosystem_Subtype_and_Total_Number_of_Bases_in_Outside_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).
NEON with Ecosystem Subtype, Total Number of Bases, and Assembly
type Outside Layer Label
ggtree(tree_bac, layout="circular", branch.length="none") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_tile,
mapping=aes(y=label, x=1, fill= AssemblyType),
offset=0.08, # The distance between external layers, default is 0.03 times of x range of tree.
pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_col,
mapping=aes(y=label, x=TotalNumberofBases),
pwidth=0.4,
axis.params=list(
axis="x", # add axis text of the layer.
text.angle=-45, # the text size of axis.
hjust=0 # adjust the horizontal position of text of axis.
),
grid.params=list() # add the grid line of the external bar plot.
) +
theme(#legend.position=c(0.96, 0.5), # the position of legend.
legend.background=element_rect(fill=NA), # the background of legend.
legend.title=element_text(size=7), # the title size of legend.
legend.text=element_text(size=6), # the text size of legend.
legend.spacing.y = unit(0.02, "cm") # the distance of legends (y orientation).
)
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.
## Warning: Removed 1709 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"Gammaproteobacteria_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 1709 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).
Gammaproteobacteria with Ecosystem Subtype, Total Number of Bases,
and Assembly type Outside Layer Label
ggtree(tree_Gammaproteobacteria, layout="circular", branch.length="none") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_tile,
mapping=aes(y=label, x=1, fill= AssemblyType),
offset=0.08, # The distance between external layers, default is 0.03 times of x range of tree.
pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_col,
mapping=aes(y=label, x=TotalNumberofBases),
pwidth=0.4,
axis.params=list(
axis="x", # add axis text of the layer.
text.angle=-45, # the text size of axis.
hjust=0 # adjust the horizontal position of text of axis.
),
grid.params=list() # add the grid line of the external bar plot.
) +
theme(#legend.position=c(0.96, 0.5), # the position of legend.
legend.background=element_rect(fill=NA), # the background of legend.
legend.title=element_text(size=7), # the title size of legend.
legend.text=element_text(size=6), # the text size of legend.
legend.spacing.y = unit(0.02, "cm") # the distance of legends (y orientation).
)
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"Gammaproteobacteria_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 123 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).
Toolik Gammaproteobacteria Highlight with Label Circular Tree
ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") +
geom_hilight(node=258, fill="grey", alpha=.6) +
geom_cladelab(node=258, label="Pseudomonadota", align=TRUE, angle='auto',
offset.text=0.5 , textcolor='black', barcolor='grey',barsize=1.5, fontsize=5)+
geom_hilight(node=259, fill="steelblue", alpha=.6) +
geom_cladelab(node=259, label="Gammaproteobacteria", align=TRUE, angle='auto', offset=0.75,
offset.text=0.5 , textcolor='black', barcolor='steelblue',barsize=1.5, fontsize=5)

ggsave(
"Toolik_Gammaproteobacteria_Highlight_with_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 14 in image
Toolik triplot with Gene and GC Content
ggtree(tree_bac_TOOL_MAGs) %<+%
NEON_MAGs_metagenomes_chemistry +
geom_tippoint(aes(colour=`Ecosystem Subtype`)) +
# For unknown reasons the following does not like blank spaces in the names
geom_facet(panel = "Gene Count", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_point,
mapping=aes(x = GeneCount))+
geom_facet(panel = "% GC Content ", data = NEON_MAGs_metagenomes_chemistry_noblank, geom = geom_col,
aes(x = GCassembled), orientation = 'y', width = .6) +
theme_tree2(legend.position=c(.1, .7))

ggsave(
"Toolik_MAGS_triplot_with_ Gene_and_GC_Content.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
Toolik with Ecosystem Subtype and Total Number of Bases in Outside
Labels
ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_tile,
mapping=aes(y=label, x=1, fill= AssemblyType),
offset=0.08, # The distance between external layers, default is 0.03 times of x range of tree.
pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
)
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.
## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"Toolik_MAGS_with_Ecosystem_Subtype_and_Total_Number_of_Bases_in_Outside_Label_Circular_Tree.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).
NEON with Ecosystem Subtype, Total Number of Bases, and Assembly
type Outside Layer Label
ggtree(tree_bac_TOOL_MAGs, layout="circular", branch.length="none") %<+%
NEON_MAGs_metagenomes_chemistry +
geom_point2(mapping=aes(color=`Ecosystem Subtype`, size=`Total Number of Bases`)) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_tile,
mapping=aes(y=label, x=1, fill= AssemblyType),
offset=0.08, # The distance between external layers, default is 0.03 times of x range of tree.
pwidth=0.25 # width of the external layer, default is 0.2 times of x range of tree.
) +
new_scale_fill() +
geom_fruit(
data=NEON_MAGs_metagenomes_chemistry_noblank,
geom=geom_col,
mapping=aes(y=label, x=TotalNumberofBases),
pwidth=0.4,
axis.params=list(
axis="x", # add axis text of the layer.
text.angle=-45, # the text size of axis.
hjust=0 # adjust the horizontal position of text of axis.
),
grid.params=list() # add the grid line of the external bar plot.
) +
theme(#legend.position=c(0.96, 0.5), # the position of legend.
legend.background=element_rect(fill=NA), # the background of legend.
legend.title=element_text(size=7), # the title size of legend.
legend.text=element_text(size=6), # the text size of legend.
legend.spacing.y = unit(0.02, "cm") # the distance of legends (y orientation).
)
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH.
## ! The following column names/name: Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Scaffold Count, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH are/is the same to tree data, the tree data column names are : label, y, angle, Site.x, Sample Name, Site ID.x, Subplot.x, Layer.x, Date.x, IMG Genome ID.x, Bin Quality, GTDB-Tk Taxonomy Lineage, Domain, Phylum, Class, Order, Family, Genus, Species, Bin Completeness, Bin Contamination, Total Number of Bases, 5s rRNA, 16s rRNA, 23s rRNA, tRNA Genes, Gene Count, Scaffold Count, Assembly Type, taxon_oid, Study Name, Site.y, Site ID.y, Subplot.y, Layer.y, Date.y, IMG Genome ID.y, GOLD Study ID, Ecosystem, Ecosystem Category, Ecosystem Subtype, Ecosystem Type, Specific Ecosystem, Altitude In Meters, Chlorophyll Concentration, Depth In Meters, Elevation In Meters, Geographic Location, Habitat, Isolation, Isolation Country, Latitude, Longhurst Code, Longhurst Description, Longitude, Nitrate Concentration, Oxygen Concentration, pH, Pressure, Salinity, Salinity Concentration, Sample Collection Date, Sample Collection Temperature, Subsurface In Meters, Genome Size * assembled, Gene Count * assembled, Scaffold Count * assembled, Genome MetaBAT Bin Count * assembled, Genome EukCC Bin Count * assembled, CRISPR Count * assembled, GC Count * assembled, GC * assembled, Coding Base Count * assembled, Coding Base Count % * assembled, CDS Count * assembled, CDS % * assembled, siteID, plotID, nlcdClass, decimalLatitude, decimalLongitude, elevation, collectionDate, horizon, soilTemp, d15N, organicd13C, nitrogenPercent, organicCPercent, CNratio, soilInWaterpH, soilInCaClpH, xmaxtmp.
## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).

ggsave(
"Toolik_MAGS_with_Ecosystem_Subtype_Total_Number_of_Bases_and_Assembly_type_Outside_Layer_Label.png",
plot = last_plot(),
device = NULL,
path = "/cloud/project/images/Plots/Lab16",
scale = 1,
width = NA,
height = NA,
units = c("in", "cm", "mm", "px"),
dpi = 300,
limitsize = TRUE,
bg = NULL,
create.dir = FALSE,
)
## Saving 12 x 12 in image
## Warning: Removed 148 rows containing missing values or values outside the scale range
## (`geom_point_g_gtree()`).